Sensitivity Analyses

The last step is re-running the analysis among mothers without pregnancy complications or physician initiated delivery that might affect gestational age. As an extra sensitivity analysis, we ask you to run the gestational age model again among the subset of term births (>=37 weeks gestation) from mothers without pregnancy complications or physician initiated delivery that might affect gestational age. Here a suggested list of variables to consider for exclusion:

• Pre-existing medical conditions in the mother:
  • diabetes (type 1, type 2)
  • hypertension
  • autoimmunediseases (including SLE, RA, and sclerodermia)
  • immuno-compromised patients
• Pregnancy complications:
  • gestational diabetes
  • placental abruption
  • placenta previa
  • pre-eclampsia/eclampsia
  • polyhydramnios, oligohydramnios
  • placental insufficiency
  • cervical insufficiency, isoimmunization,
  • cervical cerclaje
• Caesarian section, if due to pregnancy complications. C-sections due to complications during labor are kept in
• Restrict to only term births (>=37 weeks gestation)

Note: you only need to subset the phenofinal

You only need to subset the phenofinal data.frame to the samples in the given subset, the function will automatically subset the betafinal matrix and Omega matrix.

Re-running final models

Re-run the models in Step 3 among the specified subset. Be sure to change the destination folder so that you do not overwrite prior results.

Example, if running among multiple race/ethnicities

## The exclusions is going to depend on your cohort
## Gestage is expected to be in days

phenodataframe$GestageWeeks<-phenodataframe$Gestage/7

phenodataframe$NoPregnancyComplications<-"Yes"
phenodataframe$NoPregnancyComplications[which(phenodataframe$GDM == 0 &
                                                phenodataframe$PE == 0 &
                                                phenodataframe$Diabetes == 0 &
                                                phenodataframe$Hypertension == 0 &
                                                phenodataframe$Previa == 0 &
                                                phenodataframe$GestageWeeks>=37)]<-"No"


## Creating a category based on those without complications and that are among the most prevalent race/ethnicity
phenodataframe$NoPregnancyComplicationsandWhite<-"No"
phenodataframe$NoPregnancyComplicationsandWhite[which(phenodataframe$NoPregnancyComplications=="Yes" &
                                                    phenodataframe$Ethnic=="1")]<-"Yes"

tempresults<-dataAnalysis(phenofinal=phenodataframe,
                          betafinal=Betasnooutliers,
                          array="450K",
                          maxit=100,
                          robust=TRUE,
                          Omega=processedOut$Omega,
                          vartype="ExposureCont",
                          varofinterest="Gestage",
                          Table1vars=c("BWT","Gestage","PTB","Sex","Age","Parity","MaternalEd",
                                   "Smoke","preBMI","ModeDelivery","Ethnic","Meanlog2oddsContamination"),
                          StratifyTable1=FALSE,
                          StratifyTable1var=NULL,
                          adjustmentvariables=c("Sex","Age","Parity","MaternalEd",
                                   "Smoke","preBMI","ModeDelivery","Ethnic","Meanlog2oddsContamination"),
                          RunUnadjusted=TRUE,
                          RunAdjusted=TRUE,
                          RunCellTypeAdjusted=TRUE,
                          RunSexSpecific=TRUE,
                          RunCellTypeInteract=TRUE,
                          RestrictToSubset=TRUE,
                          RestrictionVar="NoPregnancyComplications",
                          RestrictToIndicator="Yes",
                          number_cores=8,
                          runparallel=TRUE,
                          destinationfolder="H:\\UCLA\\PACE\\Gestationalage-placenta",
                          savelog=TRUE,
                          cohort="HEBC",analysisdate="20220709",
                          analysisname="sensitivtyanalysis")
                          
tempresultsNonHispanicWhite<-dataAnalysis(phenofinal=phenodataframe,
                          betafinal=Betasnooutliers,
                          array="450K",
                          maxit=100,
                          Omega=processedOut$Omega,
                          vartype="ExposureCont",
                          varofinterest="Gestage",
                          Table1vars=c("BWT","Gestage","PTB","Sex","Age","Parity","MaternalEd",
                                   "Smoke","preBMI","ModeDelivery","Ethnic","Meanlog2oddsContamination"),
                          StratifyTable1=FALSE,
                          StratifyTable1var=NULL,
                          adjustmentvariables=c("Sex","Age","Parity","MaternalEd",
                                   "Smoke","preBMI","ModeDelivery","Ethnic","Meanlog2oddsContamination"),
                          RunUnadjusted=TRUE,
                          RunAdjusted=TRUE,
                          RunCellTypeAdjusted=TRUE,
                          RunSexSpecific=TRUE,
                          RunCellTypeInteract=TRUE,
                          RestrictToSubset=TRUE,
                          RestrictionVar="NoPregnancyComplicationsandWhite",
                          RestrictToIndicator="Yes",
                          number_cores=8,
                          runparallel=TRUE,
                          destinationfolder="H:\\UCLA\\PACE\\Gestationalage-placenta",
                          savelog=TRUE,
                          cohort="HEBC",analysisdate="20220709",
                          analysisname="sensitivtyanalysis")